Summary Technology for studying the higher order structure (HOS) of biomolecules encompasses some of the most important tools in all of science, and is a highlighted NIGMS research topic. Mass- spectrometric methods for studying HOS include oxidative footprinting and other methods to covalently label amino acid side-chain functional groups, and also hydrogen/deuterium exchange (HDX) on protein backbone amides. These methods require only small amounts of not-necessarily-pure material, and can study conformation and dynamics of proteins in solution with or without ligands. Mass spectrometric methods are especially well suited to biopharma comparability and epitope mapping studies. Currently, there is no software that can analyze mass spectrometric data from both chemical labeling and HDX experiments, even though the two methods both probe solvent accessibility and, if combined, would give finer resolution and greater confidence. Protein Metrics has already built beta-test software for covalent labeling, including Fast Photochemical Oxidation of Proteins (FPOP). The proposed project will focus on data analysis software for HDX experiments. The outcome will be vendor-neutral software with advanced analytical and reporting capabilities that can handle both HDX and covalent labeling experiments.